Dear All, I wonder if you could help me with this. I am trying to do some regularisation/real space refinement of a ligand with Coot. The ligand is a pseudopeptide with two non-standard aminoacids, followed by several standard ones. I assume that to do this correctly, I would need a cif file that specifies the two non-standard aa's plus the links between these two and between second and third (which is a standard one). When trying to generate a cif with a program such as eLBOW (using a pdb as the starting reference), each of the non-standard aa's gets a cif of its own, and the third, standard one, is ignored, meaning that there are no specified links between the first two (non-standard) and even less between second (non-standard) and third (standard). Coot of course keeps each aa as it should be, but breaks up the peptide chain completely.
Could you direct me how to built a cif that includes such bond specifications, starting from a reference pdb or otherwise? Is there an altogether different way of getting Coot to do what I want? Many thanks, Emmanuel Dr. Emmanuel Saridakis Researcher C Institute of Nanoscience and Nanotechnology National Centre for Scientific Research "DEMOKRITOS" 15310 Athens GREECE
